.Dd July 4, 2008
.Os "Open Babel" 2.2
.Dt babel 1 URM
.Sh NAME
.Nm babel , obabel
.Nd "a converter for chemistry and molecular modeling data files"
.Sh SYNOPSIS
.Nm
.Op Fl H Ar help-options
.Nm
.Op Ar OPTIONS
.Op Fl i Ar input-type
.Ar infile
.Op Fl o Ar output-type
.Ar outfile
.Pp
.Nm obabel
.Op Fl H Ar help-options
.Nm obabel
.Op Ar OPTIONS
.Op Fl i Ar input-type | Fl : Qo Ar SMILES-string Qc
.Ar infile
.Op Fl o Ar output-type
.Fl O Ar outfile
.Sh DESCRIPTION
.Nm
is a cross-platform program designed to interconvert
between many file formats used in molecular modeling and computational
chemistry and related areas.
.Pp
.Nm obabel
and
.Nm
are slightly different. The first is closer to the normal Unix convention
for commandline programs and more flexible when the user needs to specify
parameter values on options. With
.Nm babel
this only works when the option is the last on the line; with
.Nm obabel
no such restriction applies. It further has a shortcut for entering SMILES
strings, which can be used in place of an input file.
.Pp
Open Babel is also a complete programmers toolkit for developing 
chemistry software. For more information, se the Open Babel web pages
\%<\fBhttp://openbabel.org/\fR>.
.Sh OPTIONS
If only input and output files are given, Open Babel will guess the
file type from the filename extension.
.Bl -tag -width flag
.It Fl : Qo Ar SMILES-string Qc
Enter SMILES string and use it in place of an input file. The SMILES string
should be enclosed in quotation marks. More than one can be used, and a molecule
title can be included if enclosed in quotes.
.It Fl a Ar options
Format-specific input options. See 
.Fl H Ar format-ID 
for options allowed by a particular format
.It Fl -addtotitle
Append text to the current molecule title
.It Fl -addformula
Append the molecular formula after the current molecule title
.It Fl b
Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
.It Fl c
Center atomic coordinates at (0,0,0) 
.It Fl C
Combine molecules in first file with others having the same name
.It Fl e
Continue after errors
.It Fl d
Delete Hydrogens 
.It Fl --errorlevel Ar 2
Filter the level of errors and warnings displayed:
.br
       1 = critical errors only
       2 = include warnings too (default)
       3 = include informational messages too
       4 = include "audit log" messages of changes to data
       5 = include debugging messages too
.It Fl f Ar #
For multiple entry input, start import with molecule # as the first entry
.It Fl F
Output the available fingerprint types
.It Fl h
Add hydrogens 
.It Fl H
Output usage information 
.It Fl H Ar format-ID
Output formatting information and options for format specified
.It Fl Hall
Output formatting information and options for all formats
.It Fl i<format-ID>
Specifies input format, see below for the available formats 
.It Fl j
.It Fl -join
Join all input molecules into a single output molecule entry
.It Fl k
Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian)
.It Fl m
Produce multiple output files, to allow:
.Bl -dash -offset indent -compact
.It
Splitting one input file - put each molecule into consecutively
numbered output files
.It
Batch conversion - convert each of multiple input files into a
specified output format
.El
.It Fl l Ar #
For multiple entry input, stop import with molecule # as the last entry
.It Fl o Ar format-ID
Specifies output format, see below for the available formats 
.It Fl O Ar outfile
Specify the output file. This option applies to
.Nm obabel
only.
.It Fl p
Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
.It Fl -property 
Add or replace a property (e.g., in an MDL SD file) 
.It Fl s Ar SMARTS
Convert only molecules matching the SMARTS pattern specified 
.It Fl -separate
Separate disconnected fragments into individual molecular records
.It Fl t
All input files describe a single molecule 
.It Fl -title Ar title
Add or replace molecular title
.It Fl x Ar options
Format-specific output options. See 
.Fl H Ar format-ID
for options allowed by a particular format
.It Fl v Ar SMARTS
Convert only molecules \fBNOT\fP matching SMARTS pattern specified 
.It Fl V
Output version number and exit 
.It Fl z
Compress the output with gzip
.El
.Sh "FILE FORMATS"
The following formats are currently supported by Open Babel: 
.Bl -item -offset indent -compact
.It
acr -- Carine ASCI Crystal
.It
alc -- Alchemy format
.It
arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
.It
bgf -- MSI BGF format
.It
box -- Dock 3.5 Box format
.It
bs -- Ball and Stick format
.It
c3d1 -- Chem3D Cartesian 1 format
.It
c3d2 -- Chem3D Cartesian 2 format
.It
caccrt -- Cacao Cartesian format
.It
cache -- CAChe MolStruct format [Write-only]
.It
cacint -- Cacao Internal format [Write-only]
.It
can -- Canonical SMILES format
.It
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
.It
ccc -- CCC format [Read-only]
.It
cdx -- ChemDraw binary format [Read-only]
.It
cdxml -- ChemDraw CDXML format
.It
cht -- Chemtool format [Write-only]
.It
cif -- Crystallographic Information File
.It
cml --  Chemical Markup Language
.It
cmlr --  CML Reaction format
.It
com -- Gaussian 98/03 Cartesian Input [Write-only]
.It
copy -- Copies raw text [Write-only]
.It
crk2d -- Chemical Resource Kit 2D diagram format
.It
crk3d -- Chemical Resource Kit 3D format
.It
csr -- Accelrys/MSI Quanta CSR format [Write-only]
.It
cssr -- CSD CSSR format [Write-only]
.It
ct -- ChemDraw Connection Table format 
.It
dmol -- DMol3 coordinates format
.It
ent -- Protein Data Bank format
.It 
fa -- FASTA format [Write-only]
.It
fasta -- FASTA format [Write-only]
.It
fch -- Gaussian formatted checkpoint file format [Read-only]
.It
fchk -- Gaussian formatted checkpoint file format [Read-only]
.It
fck -- Gaussian formatted checkpoint file format [Read-only]
.It
feat -- Feature format
.It
fh -- Fenske-Hall Z-Matrix format [Write-only]
.It
fix -- SMILES FIX format [Write-only]
.It
fpt -- Fingerprint format [Write-only]
.It
fract -- Free Form Fractional format
.It
fs -- Open Babel FastSearching database
.It
fsa -- FASTA format [Write-only]
.It
g03 -- Gaussian 98/03 Output [Read-only]
.It
g98 -- Gaussian 98/03 Output [Read-only]
.It
gam -- GAMESS Output [Read-only]
.It
gamin -- GAMESS Input [Write-only]
.It
gamout -- GAMESS Output [Read-only]
.It
gau -- Gaussian 98/03 Cartesian Input [Write-only]
.It
gjc -- Gaussian 98/03 Cartesian Input [Write-only]
.It
gjf -- Gaussian 98/03 Cartesian Input [Write-only]
.It
gpr -- Ghemical format
.It
gr96 -- GROMOS96 format [Write-only]
.It
hin -- HyperChem HIN format
.It
inchi -- IUPAC InChI [Write-only]
.It
inp -- GAMESS Input [Write-only]
.It
ins -- ShelX format [Read-only]
.It
jin -- Jaguar input format [Write-only]
.It
jout -- Jaguar output format [Read-only]
.It
mdl -- MDL MOL format
.It
mmd -- MacroModel format
.It
mmod -- MacroModel format
.It
mol -- MDL MOL format
.It
mol2 -- Sybyl Mol2 format
.It
molreport -- Open Babel molecule report [Write-only]
.It
moo -- MOPAC Output format [Read-only]
.It
mop -- MOPAC Cartesian format
.It
mopcrt -- MOPAC Cartesian format
.It
mopin -- MOPAC Internal
.It
mopout -- MOPAC Output format [Read-only]
.It
mpc -- MOPAC Cartesian format
.It
mpd -- Sybyl descriptor format [Write-only]
.It
mpqc -- MPQC output format [Read-only]
.It
mpqcin -- MPQC simplified input format [Write-only]
.It
nw -- NWChem input format [Write-only]
.It
nwo -- NWChem output format [Read-only]
.It
pc --  PubChem format  [Read-only]
.It
pcm --  PCModel format
.It
pdb -- Protein Data Bank format
.It
pov -- POV-Ray input format [Write-only]
.It
pqs -- Parallel Quantum Solutions format
.It
prep -- Amber Prep format [Read-only]
.It
qcin -- Q-Chem input format [Write-only]
.It
qcout -- Q-Chem output format [Read-only]
.It
report -- Open Babel report format [Write-only]
.It
res -- ShelX format [Read-only]
.It
rxn -- MDL RXN format
.It
sd -- MDL MOL format
.It
sdf -- MDL MOL format
.It
smi -- SMILES format
.It
sy2 -- Sybyl Mol2 format
.It
tdd -- Thermo format
.It
test -- Test format [Write-only]
.It
therm -- Thermo format
.It
tmol -- TurboMole Coordinate format
.It
txyz -- Tinker MM2 format [Write-only]
.It
unixyz -- UniChem XYZ format
.It
vmol -- ViewMol format
.It
xed -- XED format [Write-only]
.It
xml --  General XML format [Read-only]
.It
xyz -- XYZ cartesian coordinates format
.It
yob -- YASARA.org YOB format
.It
zin -- ZINDO input format [Write-only]
.El
.Sh "FORMAT OPTIONS"
Individual file formats may have additional formatting options. 
.Pp
Input format options are preceded by 'a', e.g. \-as 
.Pp
Output format options are preceded by 'x', e.g. \-xn 
.Pp
For further specific information and options, use \-H<format-type>
.br
 e.g., \-Hcml
.Sh EXAMPLES
Standard conversion:
.Dl "babel \-ixyz ethanol.xyz \-opdb ethanol.pdb"
Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
.Dl "babel \-ismi \-omol2"
Split a multi-molecule file into new1.smi, new2.smi, etc.:
.Dl "babel infile.mol new.smi \-m"
.Sh SEE ALSO
.Xr obenergy 1 ,
.Xr obfit 1 ,
.Xr obgrep 1 , 
.Xr obminimize 1 , 
.Xr obprop 1 , 
.Xr obrotate 1 ,
.Xr obrotamer 1 .
The web pages for Open Babel can be found at:
\%<\fBhttp://openbabel.org/\fR> 
.Sh AUTHORS
.An -nosplit
A cast of many, including the currrent maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck , 
and innumerable others who have contributed fixes and additions. 
For more contributors to Open Babel, see 
\%<\fBhttp://openbabel.org/wiki/THANKS\fR>
.Sh COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 
.br
Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison 
.Pp
 This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
.Pp
 This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
